[ensembl-dev] variant effect predictor on bacteria genomes

[Dan Staines]

On 09/19/2012 12:24 PM, Weihong Qi wrote:
>
> Thanks. Now I got it work. The problem was I used
> "escherichia_coli_dh10b". After following your hint and set it to
> "e_coli_dh10b", it worked.
>
> For such details, while is the best place to find help information? such
> as a list of valid names to be used with --species?

Various ways - since you can use any name associated with the genome in 
the Ensembl database (e.g. e_coli_k12 or Escherichia coli K12) you can 
use the name from the web interface at bacteria.ensembl.org. 
Alternatively you can load a Registry at the public MySQL service and 
see the names of the DBAdaptors you get back, or interrogate the meta 
table of one of the core databases on the public server directly (e.g. 
select meta_value from escherichia_shigella_collection_core_15_68_5.meta 
where meta_key='species.production_name')

Hope this helps!

Dan.

-- 
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/